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Updated: Dec 20, 2025

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data
Collin Giguere1, Harsh Vardhan Dubey1, Vishal Kumar Sarsani1
1Department of Mathematics & Statistics, University of Massachusetts Amherst, 710 N. Pleasant St., Amherst, 01003, USA.
Background:
Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell or bulk tissue. Yet, there does not yet exist a tool for simulating DNA sequencing data from such a nested sampling arrangement with single-cell and bulk samples so that developers of analysis methods can assess accuracy and precision.
Results:
We have developed a tool that simulates DNA sequencing data from hierarchically grouped (correlated) samples where each sample is designated bulk or single-cell. Our tool uses a simple configuration file to define the experimental arrangement and can be integrated into software pipelines for testing of variant callers or other genomic tools.
Conclusions:
The DNA sequencing data generated by our simulator is representative of real data and integrates seamlessly with standard downstream analysis tools.
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